FIG 4.

Genome-wide screening of LANA, KAP1, Sin3A, HIF-1α, RTA, and RBP-Jκ binding sites within the KSHV genome. (A) (ChIP) assay was done by real-time PCR using a genome-wide array of 100 pair primers spaced across the KSHV genome using specific antibody as indicated. The enrichment of specific antibody bound to DNA was calculated by compared with input DNA and verified by an affinity more than 2-fold higher than for the nonspecific IgG parallel control. Graphs represent means ± standard deviations of two independent experiments. Chromatin DNA were prepared from KSHV-positive cell lines BC3 and BCBL1 with 21% (normoxia) or 1% (hypoxia) oxygen treatment for overnight before harvest. The results reveal four hypoxia-responsive clusters (HRC I, II, III, and IV) within the KSHV genome based on the HIF-1α–DNA binding region during hypoxia and indicated in light green. The main genes within these four clusters are shown in Fig. 5A. (B) Summary of KSHV whole-genome peak analysis for LANA, KAP1, Sin3A, HIF-1α, RBP-Jκ, and RTA binding chromatin from BC3 and BCBL1 cells under normoxic and hypoxic conditions. The amount of each protein binding site on KSHV genome is summarized as fold more than 2 from panel A, in parentheses.